(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)<br>

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[[Image:CAM000423.jpg]] <br>

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Here's the OpenPCR machine as it looks when hooked up to the computer and running. Made up of thin pieces of wood, the case contains the hardware of the machine. A second, smaller wood case on top of the main case contains the loading bay, which acts as a lid. Small test vials can be placed into holders here in the bay to be heated by the PCR machine. Inside the main body of the machine sits the hardware similar to a personal computer. A processor unit connects to the heating hardware as well as the power supply and LED display board. Above the power supply lies the heatsink, with a fan attached, facing vents in the case, which allows for efficient thermal control inside the machine to prevent overheating. The machine then has sockets that allow the machine to be hooked up by USB to a computer. Using a computer the PCR can be ordered to heat up the vials in the heating lid on certain intervals at different temperatures as well as indicated cycles.<br>

When we unplugged (part 3) from (part 6), the display of the machine turned off.

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When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)

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When we unplugged the white wire that connects (part 6) to (part 2), the machine's temperature display dropped to a reading of -40°C.

'''Test Run'''

'''Test Run'''

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(Write the date you first tested Open PCR and your experience(s) with the machine)<br>

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The Open PCR machine was first tested on March 5th as part of the introductory lessons for the week 10 Open PCR trials. For us, this testing did not go well at all. In spite of trying several of the machines and several USB cables, we were unable to complete a working trial run. We completed the activities associated with disassembling and reassembling the machine, but we had to observe other groups to find the proper data from the testing. In the second week, we discovered that our issue was with the USB ports on the computer, not the Open PCR machine, so all of these issues from testing were resolved in time for the actual experiment.<br>

First the DNA/Primer mix is combined with the PCR reaction mix in a small test tube. Repeat samples are advised to make sure that the results are consistent.

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DNA Template <br>

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When the test tube is placed in a PCR machine, the mixture is heated to 95 degrees Celsius for 30 seconds. This high heat breaks apart complementary strands of DNA, exposing the nucleotides. The DNA strands are essentially cut in half lengthwise into two new strands.

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DNA Polymerase<br>

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DNA Primers<br>

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Nucleotides<br>

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Procedure:<br>

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The machine then rapidly cools to 57 degrees Celsius for 30 seconds, allowing the DNA primers to bind to the exposed sites. The DNA primers can only bind to the specific site they are complementary to, which allows researchers to target specific DNA sequences. Even if only one nucleotide is different, the primer does not bind well enough to stay. This means that researchers can choose a specific gene, such as one predisposing for cancer, and order a primer that binds only to that gene. If the specified gene is not present, the primer will not bind and the DNA will not be amplified.

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First, the components are combined and heated. Once the reaction is heated to a temperature of 95 degrees Celsius, the hydrogen bonds between the DNA strands break and create two separate DNA sequences. After that, leave it to cool down to a temperature of around 55 degrees Celsius. As it cools, the DNA primers are able to hybridize to the separate DNA strands. The DNA polymerase is going the bind the DNA sequence with the DNA Primer. Once, the DNA polymerase is bound, it is going to take some of the free nucleotides from the surrounding area and complete the DNA strand. The result is a two separate DNA sequences, with two DNA strand identical to the first one. Repeatedly doing the steps and the result amount of DNA stands

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Two different primers are needed: a forward primer and reverse primer. The forward primer binds to one "half" of the DNA sample, and the reverse primer binds to the other "half." If you picture the DNA as a train track, with each rail as one half of the DNA, one primer binds to one rail, and the other binds to the other rail at the opposite end of the track.

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The mixture is then heated up to 72 degrees Celsius for 30 seconds. At this temperature, DNA polymerase binds to the primers and builds a new segment of complementary DNA with the free nucleotides in the mixture. Returning to the train track analogy, one rail is being built from right to left and the other from left to right, both being built towards each other. This is because DNA is read in one direction on one side, and a different direction (relative to the first) on the other.

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So, if there was only one strand of DNA in the mixture originally, now there are two (since both halves have been replicated). The mixture is then reheated to 95 degrees and the cycle continues, each time doubling the amount of DNA in the mixture. This process usually continues for an hour or so, until there are billions of copies of DNA. This whole process is referred to as DNA amplification.

LAB 1 WRITE-UP

Initial Machine Testing

The Original Design

Here's the OpenPCR machine as it looks when hooked up to the computer and running. Made up of thin pieces of wood, the case contains the hardware of the machine. A second, smaller wood case on top of the main case contains the loading bay, which acts as a lid. Small test vials can be placed into holders here in the bay to be heated by the PCR machine. Inside the main body of the machine sits the hardware similar to a personal computer. A processor unit connects to the heating hardware as well as the power supply and LED display board. Above the power supply lies the heatsink, with a fan attached, facing vents in the case, which allows for efficient thermal control inside the machine to prevent overheating. The machine then has sockets that allow the machine to be hooked up by USB to a computer. Using a computer the PCR can be ordered to heat up the vials in the heating lid on certain intervals at different temperatures as well as indicated cycles.

Experimenting With the Connections

When we unplugged (part 3) from (part 6), the display of the machine turned off.

When we unplugged the white wire that connects (part 6) to (part 2), the machine's temperature display dropped to a reading of -40°C.

Test Run

The Open PCR machine was first tested on March 5th as part of the introductory lessons for the week 10 Open PCR trials. For us, this testing did not go well at all. In spite of trying several of the machines and several USB cables, we were unable to complete a working trial run. We completed the activities associated with disassembling and reassembling the machine, but we had to observe other groups to find the proper data from the testing. In the second week, we discovered that our issue was with the USB ports on the computer, not the Open PCR machine, so all of these issues from testing were resolved in time for the actual experiment.

Research and Development

First the DNA/Primer mix is combined with the PCR reaction mix in a small test tube. Repeat samples are advised to make sure that the results are consistent.

When the test tube is placed in a PCR machine, the mixture is heated to 95 degrees Celsius for 30 seconds. This high heat breaks apart complementary strands of DNA, exposing the nucleotides. The DNA strands are essentially cut in half lengthwise into two new strands.

The machine then rapidly cools to 57 degrees Celsius for 30 seconds, allowing the DNA primers to bind to the exposed sites. The DNA primers can only bind to the specific site they are complementary to, which allows researchers to target specific DNA sequences. Even if only one nucleotide is different, the primer does not bind well enough to stay. This means that researchers can choose a specific gene, such as one predisposing for cancer, and order a primer that binds only to that gene. If the specified gene is not present, the primer will not bind and the DNA will not be amplified.

Two different primers are needed: a forward primer and reverse primer. The forward primer binds to one "half" of the DNA sample, and the reverse primer binds to the other "half." If you picture the DNA as a train track, with each rail as one half of the DNA, one primer binds to one rail, and the other binds to the other rail at the opposite end of the track.

The mixture is then heated up to 72 degrees Celsius for 30 seconds. At this temperature, DNA polymerase binds to the primers and builds a new segment of complementary DNA with the free nucleotides in the mixture. Returning to the train track analogy, one rail is being built from right to left and the other from left to right, both being built towards each other. This is because DNA is read in one direction on one side, and a different direction (relative to the first) on the other.

So, if there was only one strand of DNA in the mixture originally, now there are two (since both halves have been replicated). The mixture is then reheated to 95 degrees and the cycle continues, each time doubling the amount of DNA in the mixture. This process usually continues for an hour or so, until there are billions of copies of DNA. This whole process is referred to as DNA amplification.

(Add a write-up of the information discussed in Week 3's class)

(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)